How to configure the settings for different tools

[ChunfangZheng]

metAMOS is a well-designed pipeline for analyzing metagenomic data. However, when a user starts to run metAMOS on a cluster, it is not clear for the user to know how to change settings for different tools included by metAMOS. I have noticed that some settings are hard-coded in the scripts, and some are in the .spec file located under the folder of Utilities/config. Do you have any suggestion for a user to keep/modify his own copy of the settings? or is it possible to add this feature to metAMOS if metAMOS doesn't have this feature?